- recipe bioconductor-recoup
An R package for the creation of complex genomic profile plots
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/recoup.html
- License:
GPL (>= 3)
- Recipe:
- Links:
biotools: recoup, doi: 10.1038/nmeth.3252
recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.
- package bioconductor-recoup¶
- versions:
1.30.0-0
,1.28.0-0
,1.26.0-0
,1.22.0-0
,1.20.0-0
,1.18.0-1
,1.18.0-0
,1.16.0-0
,1.14.0-0
,1.30.0-0
,1.28.0-0
,1.26.0-0
,1.22.0-0
,1.20.0-0
,1.18.0-1
,1.18.0-0
,1.16.0-0
,1.14.0-0
,1.12.0-1
,1.10.0-0
,1.8.0-0
,1.6.0-0
,1.4.0-0
- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0
- depends bioconductor-biomart:
>=2.58.0,<2.59.0
- depends bioconductor-biostrings:
>=2.70.0,<2.71.0
- depends bioconductor-complexheatmap:
>=2.18.0,<2.19.0
- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0
- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0
- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0
- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0
- depends bioconductor-iranges:
>=2.36.0,<2.37.0
- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0
- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0
- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0
- depends r-base:
>=4.3,<4.4.0a0
- depends r-circlize:
- depends r-ggplot2:
- depends r-httr:
- depends r-rsqlite:
- depends r-stringr:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-recoup and update with:: mamba update bioconductor-recoup
To create a new environment, run:
mamba create --name myenvname bioconductor-recoup
with
myenvname
being a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-recoup:<tag> (see `bioconductor-recoup/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-recoup/README.html)